iqtree

phylogenetic analysis tool for maximum likelihood tree inference

TLDR

Run phylogenetic analysis

$ iqtree -s [alignment.fasta]

Specify model

$ iqtree -s [alignment.fasta] -m [GTR+G]

Automatic model selection

$ iqtree -s [alignment.fasta] -m MFP

Standard bootstrap analysis

$ iqtree -s [alignment.fasta] -b [1000]

Ultra-fast bootstrap (IQ-TREE2 uses -B)

$ iqtree -s [alignment.fasta] -B [1000]

Use multiple threads (IQ-TREE2 uses -T)

$ iqtree -s [alignment.fasta] -T [4]

IQ-TREE is a phylogenetic analysis tool for maximum likelihood tree inference. It supports various substitution models, model selection, and multiple bootstrap methods.IQ-TREE is known for its speed and accuracy, implementing efficient algorithms for large-scale phylogenetic analysis. It handles DNA, protein, codon, and morphological data.

PARAMETERS

-s file

Input alignment file.

-m model

Substitution model (or MFP for selection).

-b n

Standard bootstrap replicates.

-B, --ufboot n

Ultra-fast bootstrap replicates (minimum 1000). IQ-TREE v1 used -bb.

-T, --threads n|AUTO

Number of CPU threads, or AUTO to auto-detect. IQ-TREE v1 used -nt.

-pre prefix

Output file prefix.

-o taxa

Outgroup taxa.

-t tree

Starting tree file.

-wbt

Write bootstrap trees.

--bnni

Optimize UFBoot trees by NNI on bootstrap alignment (reduces overestimation).

-alrt n

SH-like approximate likelihood ratio test.

OUTPUT FILES

$ .treefile    Best tree in Newick format
.iqtree      Analysis report
.log         Screen log
.mldist      ML distances
.bionj       BIONJ starting tree

CAVEATS

Large alignments require significant memory. Model selection can be time-consuming. Bootstrap numbers vary by study requirements.

HISTORY

IQ-TREE was developed by Bui Quang Minh, Lam-Tung Nguyen, and Arndt von Haeseler at the University of Vienna. First released in 2014, it's become a standard tool for molecular phylogenetics.